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Fixed up the comments in the GATKReportTable code and added some sanity checks to make sure that the user doesn't inconsistently add rows and corresponding IDs to the table.

This commit is contained in:
Eric Banks 2012-05-21 14:16:13 -04:00
parent 27c46b8071
commit 7f5ec17d22
1 changed files with 39 additions and 12 deletions
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51
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -81,6 +81,13 @@ public class GATKReportTable {
public int index() { return index; }
}
/**
* Construct a new GATK report table from the reader
* Note that the row ID mappings are just the index -> index
*
* @param reader the reader
* @param version the GATK report version
*/
public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
switch ( version ) {
@ -271,8 +278,16 @@ public class GATKReportTable {
}
/**
* Add a column to the report and specify the default value that should be supplied if a given position in the table
* is never explicitly set.
* Remove a mapping from ID to row index.
*
* @param ID the row ID
*/
public void removeRowIDMapping(final Object ID) {
rowIdToIndex.remove(ID);
}
/**
* Add a column to the report
*
* @param columnName the name of the column
*/
@ -281,9 +296,7 @@ public class GATKReportTable {
}
/**
* Add a column to the report, specify the default column value, whether the column should be displayed in the final
* output (useful when intermediate columns are necessary for later calculations, but are not required to be in the
* output file), and the format string used to display the data.
* Add a column to the report and the format string used to display the data.
*
* @param columnName the name of the column
* @param format the format string used to display data
@ -305,7 +318,7 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
* expand the underlying table if needed to include the given row index
*
* @param rowIndex the row index
* @param updateRowIdMap should we update the row ID map?
@ -324,7 +337,8 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
* Set the value for a given position in the table.
* If the row ID doesn't exist, it will create a new row in the table with the given ID.
*
* @param rowID the row ID
* @param columnName the name of the column
@ -338,6 +352,14 @@ public class GATKReportTable {
set(rowIdToIndex.get(rowID), columnNameToIndex.get(columnName), value);
}
/**
* Set the value for a given position in the table.
* If the row index doesn't exist, it will create new rows in the table accordingly.
*
* @param rowIndex the row index
* @param colIndex the column index
* @param value the value to set
*/
public void set(final int rowIndex, final int colIndex, Object value) {
expandTo(rowIndex, true);
verifyEntry(rowIndex, colIndex);
@ -375,11 +397,12 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
*
* @param rowID the row ID
* @param columnName the name of the column
*/
* Increment the value for a given position in the table.
* Throws an exception if the value in the cell is not an integer.
*
* @param rowID the row ID
* @param columnName the name of the column
*/
public void increment(final Object rowID, final String columnName) {
int prevValue;
if ( !rowIdToIndex.containsKey(rowID) ) {
@ -518,6 +541,10 @@ public class GATKReportTable {
// write the table body
if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);